An unlabelled peptide expression data file called “pep_edata.csv” was uploaded to pmart. The protein data was rolled-up from peptide data. The column that designates unique molecules was marked as “Protein”. The original scale of the data was log2 and remained unchanged. The value to denote missing data was “NA” and the expression data was not already normalized.
An associated biomolecule information file was also uploaded called pep_emeta.csv and the protein identifier column was designated as Protein.
An associated sample information file was also uploaded called “pep_fdata.csv”. Trimmed sample names were not used. The column in the sample information file which indicates sample names was designated as “SampleID”.
This table summarizes all the user specified main effects or covariates in pmart. The “Selected Column Name” denotes the name of the column in the sample information file assigned as a main effect or covariate.
| Main Effect or Covariate | Selected Column Name |
|---|---|
| First Main Effect | Condition |
| Second Main Effect | None selected |
| First Covariate | None selected |
| Second Covariate | None selected |
The first column in the table below denotes a property of the peptide data, and the “Data” column states that property’s value.
| Data | |
|---|---|
| Class | proData |
| Unique SampleIDs (f_data) | 11 |
| Unique Proteins (e_data) | 1736 |
| Unique Proteins (e_meta) | NA |
| Missing Observations | 13741 |
| Proportion Missing | 0.72 |
In the table below, the first column denotes the sample and the second is the missing number of observations. The third column represents the second as a percentage of the total number of observations for that sample.
| Missing Observations | Proportion Missing | |
|---|---|---|
| Infection1 | 1151 | 0.663 |
| Infection2 | 1127 | 0.649 |
| Infection3 | 1308 | 0.753 |
| Infection4 | 1366 | 0.787 |
| Infection6 | 1293 | 0.745 |
| Infection7 | 1248 | 0.719 |
| Infection8 | 1568 | 0.903 |
| Infection9 | 1511 | 0.870 |
| Mock1 | 1079 | 0.622 |
| Mock2 | 1049 | 0.604 |
| Mock3 | 1041 | 0.600 |
Filters were not applied.
Molecule filters were not applied to the data.
CV filters were not applied to the data.
imd-ANOVA filters were not applied to the data.
Proteomics filters were not applied to the data.
rMD filters were not applied to the data.
Custom filters were not applied to the data.
Peptide data was normalized.
SPANS was run to determine optimum normalization parameters.
Manual normalization was not used to normalize the data.
Protein Roll-Up was conducted.
Protein quantification was conducted with the rrollup method and was centered with the median. The quantile cutoff was restricted to 0.
The statistical analysis step was run.
The following groups were compared: Mock_vs_Infection. Reported below are the parameters used in the statistical analysis, followed by the number of siginificant biomolecules for each comparison.
| Attribute | Value |
|---|---|
| Test Method | anova |
| Multiple Comparison Adjustment | holm |
| Significance Threshold | 0.05 |
| Comparison | Up_total | Down_total | Up_anova | Down_anova | Up_gtest | Down_gtest | |
|---|---|---|---|---|---|---|---|
| Mock_vs_Infection | Mock_vs_Infection | 718 | 328 | 718 | 328 | 0 | 0 |